Cut it in half lengthwise and place rind side up on a baking sheet. (If you have trouble cutting the squash you might consider microwaving for a couple of minutes just to soften a bit before baking.) Pour enough water in the pan to come up about 1/4”. Bake for 45 minutes and allow to cool.
Scoop out the seeds and membranes from each side of the squash. (I find it easier to do after baking but some people do it before)
Use a fork to “shred” the flesh of the spaghetti squash -set aside.
Heat butter in a medium/large pan. Mmmm butter….
Add the finely diced onions to the pan and sauté until translucent (approximately 12 minutes). Stir in the salt, pepper and nutmeg.
Add the Greek yogurt, spaghetti squash and 3/4 cup of the Gruyère to the pan, stirring to combine, and heat for a couple of minutes on medium.
Pour the mixture into a baking dish and spread it evenly.
Top with the remaining 1/2 cup of grated cheese and bake for 30 minutes until hot and bubbling. If the top is not browned you can broil on high for a few minutes until the Gruyère cheese is nicely toasted.